PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT2G45420.1

Common Name

ASL20, F4L23.7, LBD18

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

LBD

Protein Properties

Length: 262aa MW: 27218.6 Da PI: 8.0852

Description

LOB domain-containing protein 18

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT2G45420.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	128.5	3e-40	37	137	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelall 97 +C aCk+lrrkC+++C++apyf +eq ++ fa+vhk+FGasnv+kll ++p ++r+da+ +++yeA+ar+rdP+yG+v++i++lqqq+ +l+ae+++l AT2G45420.1 37 PCGACKFLRRKCVPGCIFAPYFDSEQgSAYFAAVHKVFGASNVSKLLLHIPVHRRSDAVVTICYEAQARIRDPIYGCVAHIFALQQQVVNLQAEVSYL 134 7*********************998899****************************************************************99 PP DUF260 98 kee 100 +++ AT2G45420.1 135 QAH 137 986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PIRSF	PIRSF038127	6.8E-139	1	262	IPR017394	LOB domain-containing protein 18/20
PROSITE profile	PS50891	22.866	36	138	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	2.9E-39	37	135	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010089	Biological Process	xylem development
GO:0010311	Biological Process	lateral root formation
GO:0005634	Cellular Component	nucleus

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000084	anatomy	plant sperm cell
PO:0000290	anatomy	tracheary element

Sequence ? help Back to Top
Protein Sequence Length: 262 aa Download sequence Send to blast
MSGGGNTITA VGGGGGGCGG GGSSGGGGSS GGGGGGPCGA CKFLRRKCVP GCIFAPYFDS 60 EQGSAYFAAV HKVFGASNVS KLLLHIPVHR RSDAVVTICY EAQARIRDPI YGCVAHIFAL 120 QQQVVNLQAE VSYLQAHLAS LELPQPQTRP QPMPQPQPLF FTPPPPLAIT DLPASVSPLP 180 STYDLASIFD QTTSSSAWAT QQRRFIDPRH QYGVSSSSSS VAVGLGGENS HDLQALAHEL 240 LHRQGSPPPA ATDHSPSRTM SR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	7e-39	33	138	7	111	LOB family transfactor Ramosa2.1
5ly0_B	7e-39	33	138	7	111	LOB family transfactor Ramosa2.1
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.21365	0.0	seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	42570426	0.0
Genevisible	245140_at	0.0
Expression Atlas	AT2G45420	-
AtGenExpress	AT2G45420	-
ATTED-II	AT2G45420	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: During lateral root formation, expressed in the lateral root primordia, and the developing, emerged, and mature lateral roots. {ECO:0000269\|PubMed:19717544}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots, stems, leaves and flowers (PubMed:12068116, PubMed:24484953). Expressed in vascular tissues of hypocotyls, leaves, roots, developing floral organs and siliques (PubMed:19088331). {ECO:0000269\|PubMed:12068116, ECO:0000269\|PubMed:19088331, ECO:0000269\|PubMed:24484953}.

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the positive regulation of tracheary element (TE) differentiation. Involved in a positive feedback loop that maintains or promotes NAC030/VND7 expression that regulates TE differentiation-related genes (PubMed:19088331). Functions in the initiation and emergence of lateral roots, in conjunction with LBD16, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Transcriptional activator that directly regulates EXPA14, a gene encoding a cell wall-loosening factor that promotes lateral root emergence. Activates EXPA14 by directly binding to a specific region of its promoter (PubMed:22974309). Transcriptional activator that directly regulates EXPA17, a gene encoding a cell wall-loosening factor that promotes lateral root emergence (PubMed:23872272). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269\|PubMed:19088331, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:22974309, ECO:0000269\|PubMed:23749813, ECO:0000269\|PubMed:23872272, ECO:0000269\|PubMed:26059335}.

Function -- GeneRIF ? help Back to Top
LBD16 and LBD18 might function in a combinatorial manner in lateral root formation. [PMID: 19717544] E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn, regulated by the auxin signaling pathway. [PMID: 22003076] Data show that overexpression of each of the LBD genes promotes callus formation in the absence of exogenous phytohormones, while suppression of LBD function inhibits the callus induction process. [PMID: 22508267] LBD16, LBD29, and LBD18 are involved in cell cycle progression of the pericycle in response to auxin. [PMID: 22699776] This study revealed the molecular function of LBD18 as a specific DNA-binding transcription factor that activates EXP14 expression by directly binding to its promoter. [PMID: 22974309] the proline mutation completely abolished LBD18 DNA-binding activity. [PMID: 23430048] PUCHI co-acts with LBD16 and LBD18 to control lateral root primordium development and lateral root emergence. [PMID: 23749813] Results suggest that LBD18 up-regulates EXPA17 to enhance cell separation to promote lateral roots (LRs) emergence in Arabidopsis. [PMID: 23872272] GBF INTERACTING PROTEIN1 (GIP1) interacts with LBD18 in yeast and Arabidopsis protoplasts. Reverse-transcription-pcr analysis showed overlapping expression of GIP1 and LBD18 in roots, aerial parts, and rosette leaves of Arabidopsis. [PMID: 24484953] Results suggest that Lateral Organ Boundaries Domain16 and 18 (LBD16 and LBD18) are important regulators of lateral root (LR) initiation and development downstream of AUXIN1 (AUX1) and LIKE-AUXIN3 (LAX3) auxin influx carriers. [PMID: 26059335] Data show that the conserved Leu or valine residues in the coiled-coil motif are critical for the dimerization of LBD16 or LBD18 transcription factors. [PMID: 28336771] conserved Leu or Val residues in the coiled-coil motifs of LBD16 and LBD18 are critical for their dimerization as well as the transcriptional regulation to display their biological functions. [PMID: 29227192] uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity [PMID: 29681137] acts downstream of ARF7 and ARF19 in formation of adventitious roots [PMID: 30704405]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00314	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT2G45420.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:23749813}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT5G20730 (A)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	auxin

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT2G45420

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Reduced number of lateral roots. {ECO:0000269\|PubMed:19717544}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT2G45420

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB473853	0.0	AB473853.1 Arabidopsis thaliana ASL20 mRNA for ASYMMETRIC LEAVES2-like 20 protein, complete cds.
GenBank	AF447891	0.0	AF447891.1 Arabidopsis thaliana LOB DOMAIN 18 (LBD18) mRNA, complete cds.
GenBank	BT025716	0.0	BT025716.1 Arabidopsis thaliana At2g45420 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_850436.1	0.0	LOB domain-containing protein 18
Swissprot	O22131	0.0	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	A0A178VVX7	0.0	A0A178VVX7_ARATH; LBD18
STRING	AT2G45420.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM108	28	359
Representative plant	OGRP405	15	100

Link Out ? help Back to Top
Phytozome	AT2G45420.1
Entrez Gene	819150
iHOP	AT2G45420
wikigenes	AT2G45420

Publications ? help Back to Top
Iwakawa H, et al. The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana, required for formation of a symmetric flat leaf lamina, encodes a member of a novel family of proteins characterized by cysteine repeats and a leucine zipper. Plant Cell Physiol., 2002. 43(5): p. 467-78 [PMID:12040093] Shuai B,Reynaga-Peña CG,Springer PS The lateral organ boundaries gene defines a novel, plant-specific gene family. Plant Physiol., 2002. 129(2): p. 747-61 [PMID:12068116] Goda H, et al. Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis. Plant Physiol., 2004. 134(4): p. 1555-73 [PMID:15047898] Redman JC,Haas BJ,Tanimoto G,Town CD Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J., 2004. 38(3): p. 545-61 [PMID:15086809] Okushima Y, et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell, 2005. 17(2): p. 444-63 [PMID:15659631] Soyano T,Thitamadee S,Machida Y,Chua NH ASYMMETRIC LEAVES2-LIKE19/LATERAL ORGAN BOUNDARIES DOMAIN30 and ASL20/LBD18 regulate tracheary element differentiation in Arabidopsis. Plant Cell, 2008. 20(12): p. 3359-73 [PMID:19088331] Matsumura Y,Iwakawa H,Machida Y,Machida C Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members. Plant J., 2009. 58(3): p. 525-37 [PMID:19154202] Lee DJ,Park JW,Lee HW,Kim J Genome-wide analysis of the auxin-responsive transcriptome downstream of iaa1 and its expression analysis reveal the diversity and complexity of auxin-regulated gene expression. J. Exp. Bot., 2009. 60(13): p. 3935-57 [PMID:19654206] Lee HW,Kim NY,Lee DJ,Kim J LBD18/ASL20 regulates lateral root formation in combination with LBD16/ASL18 downstream of ARF7 and ARF19 in Arabidopsis. Plant Physiol., 2009. 151(3): p. 1377-89 [PMID:19717544] Berckmans B, et al. Auxin-dependent cell cycle reactivation through transcriptional regulation of Arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell, 2011. 23(10): p. 3671-83 [PMID:22003076] Fan M,Xu C,Xu K,Hu Y LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration. Cell Res., 2012. 22(7): p. 1169-80 [PMID:22508267] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Feng Z,Zhu J,Du X,Cui X Effects of three auxin-inducible LBD members on lateral root formation in Arabidopsis thaliana. Planta, 2012. 236(4): p. 1227-37 [PMID:22699776] Lee HW,Kim MJ,Kim NY,Lee SH,Kim J LBD18 acts as a transcriptional activator that directly binds to the EXPANSIN14 promoter in promoting lateral root emergence of Arabidopsis. Plant J., 2013. 73(2): p. 212-24 [PMID:22974309] Osakabe Y, et al. Osmotic stress responses and plant growth controlled by potassium transporters in Arabidopsis. Plant Cell, 2013. 25(2): p. 609-24 [PMID:23396830] Lee HW,Kim MJ,Park MY,Han KH,Kim J The conserved proline residue in the LOB domain of LBD18 is critical for DNA-binding and biological function. Mol Plant, 2013. 6(5): p. 1722-5 [PMID:23430048] Kang NY,Lee HW,Kim J The AP2/EREBP gene PUCHI Co-Acts with LBD16/ASL18 and LBD18/ASL20 downstream of ARF7 and ARF19 to regulate lateral root development in Arabidopsis. Plant Cell Physiol., 2013. 54(8): p. 1326-34 [PMID:23749813] Lee HW,Kim J EXPANSINA17 up-regulated by LBD18/ASL20 promotes lateral root formation during the auxin response. Plant Cell Physiol., 2013. 54(10): p. 1600-11 [PMID:23872272] Lee HW,Park JH,Park MY,Kim J GIP1 may act as a coactivator that enhances transcriptional activity of LBD18 in Arabidopsis. J. Plant Physiol., 2014. 171(5): p. 14-8 [PMID:24484953] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Lee HW,Cho C,Kim J Lateral Organ Boundaries Domain16 and 18 Act Downstream of the AUXIN1 and LIKE-AUXIN3 Auxin Influx Carriers to Control Lateral Root Development in Arabidopsis. Plant Physiol., 2015. 168(4): p. 1792-806 [PMID:26059335] Lee HW, et al. Dimerization in LBD16 and LBD18 Transcription Factors Is Critical for Lateral Root Formation. Plant Physiol., 2017. 174(1): p. 301-311 [PMID:28336771] Pandey SK,Kim J Coiled-coil motif in LBD16 and LBD18 transcription factors are critical for dimerization and biological function in arabidopsis. Plant Signal Behav, 2018. 13(1): p. e1411450 [PMID:29227192] Pandey SK, et al. LBD18 uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity in Arabidopsis. Plant J., 2018. 95(2): p. 233-251 [PMID:29681137] Lee HW, et al. LBD16 and LBD18 acting downstream of ARF7 and ARF19 are involved in adventitious root formation in Arabidopsis. BMC Plant Biol., 2019. 19(1): p. 46 [PMID:30704405]